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Stop smart stack infinietly looping

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This commit is contained in:
Julian Stirling 2025-06-27 01:11:55 +01:00
parent e90ff73499
commit 73e54b802b
3 changed files with 35 additions and 20 deletions
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29
src/openflexure_microscope_server/things/autofocus.py
View file

@ -26,8 +26,6 @@ from .camera import RawCameraDependency as Camera
from .camera import CameraDependency as WrappedCamera
from .stage import StageDependency as Stage
# TODO Capture reolution should be save resolution for consistency
class StackParams:
"""A class for holding for scan parameters
@ -76,26 +74,29 @@ class StackParams:
# attributed to be documented
settling_time: float = 0.3
"""time (in seconds) between moving and capturing an image"""
"""Time (in seconds) between moving and capturing an image"""
backlash_correction: int = 250
"""
distance (in steps) to overshoot a move and then undo, to account for backlash
Distance (in steps) to overshoot a move and then undo, to account for backlash
"""
stack_height_limit: int = 15
"""
how many images can be appended to the stack after the predicted peak to test
How many images can be appended to the stack after the predicted peak to test
for focus before assuming the focus was passed, and restarting the stack
"""
img_undershoot: int = 5
"""
how far below (in factors of stack_dz) the estimated optimal starting position to
How far below (in factors of stack_dz) the estimated optimal starting position to
begin the stack. Better to start slightly too low and require many images, rather
than too high and needing to autofocus and restart the stack
"""
max_attempts: int = 3
"""Maximum number of times to attempt fast stack"""
@property
def stack_z_range(self) -> int:
"""The range of the z stack, in steps
@ -129,7 +130,8 @@ class StackParams:
"""Return the slice of images to save given the index of the sharpest image"""
images_each_side = (self.images_to_save - 1) // 2
return slice(
sharpest_index - images_each_side, sharpest_index + images_each_side + 1
max(sharpest_index - images_each_side, 0),
sharpest_index + images_each_side + 1,
)
@ -427,7 +429,7 @@ class AutofocusThing(Thing):
images_dir: str,
autofocus_dz: int,
save_resolution: tuple[int, int],
) -> None:
) -> tuple[bool, int]:
"""Run a smart stack, which captures images offset in z, testing
whether the sharpest image is towards the centre of the stack.
The sharpest image, and optionally images around the sharpest,
@ -440,6 +442,7 @@ class AutofocusThing(Thing):
LabThings FastAPI
Returns:
A boolean, True if stack was successfully
The z position of the sharpest image
"""
@ -453,9 +456,9 @@ class AutofocusThing(Thing):
save_resolution=save_resolution,
)
success = False
trys = 0
# Loop until a stack is successful
while not success: # TODO add a maximum number?
while trys < stack_parameters.max_attempts:
success, captures, sharpest_id = self.z_stack(
stack_parameters=stack_parameters,
stage=stage,
@ -475,7 +478,9 @@ class AutofocusThing(Thing):
sharpness_monitor,
)
# Save the sharpest image, and images either side of focus
# Save stack_parameters.image_to_save images centred on the sharpest capture.
# If the smart_stack failed the exact number of images saved may not be
# stack_parameters.image_to_save
self.save_stack(
sharpest_id=sharpest_id,
captures=captures,
@ -484,7 +489,7 @@ class AutofocusThing(Thing):
)
# Return the z position of the sharpest image, for path planning and tracking
return _get_capture_by_id(captures, sharpest_id).position["z"]
return success, _get_capture_by_id(captures, sharpest_id).position["z"]
def reset_stack(
self,

10
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -653,20 +653,16 @@ class SmartScanThing(Thing):
self._scan_logger.info(msg)
continue
focused_height = self._autofocus.run_smart_stack(
focused, focused_height = self._autofocus.run_smart_stack(
images_dir=self._ongoing_scan_images_dir,
autofocus_dz=self._scan_data["autofocus_dz"],
save_resolution=self._scan_data["save_resolution"],
)
current_pos_xyz = (
new_pos_xyz[0],
new_pos_xyz[1],
focused_height,
)
current_pos_xyz = (new_pos_xyz[0], new_pos_xyz[1], focused_height)
route_planner.mark_location_visited(
current_pos_xyz, imaged=True, focused=True
current_pos_xyz, imaged=True, focused=focused
)
# increment capure counter as thread has completed

16
tests/test_stack.py
View file

@ -170,9 +170,23 @@ def test_computed_stack_params():
sharpnesses = [50, 77, 234, 324, 390, 496, 569, 454, 333, 222, 178, 70]
max_ind = np.argmax(sharpnesses)
slice_to_save = stack_parameters.slice_to_save(max_ind)
# Check the slice corresponds to the inex for the 5 images centred on the sharpest
# Check the slice corresponds to the index for the 5 images centred on the sharpest
assert sharpnesses[slice_to_save] == [390, 496, 569, 454, 333]
# For a failed smart stack the slice may be truncated. Check it truncates correctly
sharpnesses = [496, 569, 454, 333, 222, 178, 70, 69, 66, 50, 45, 40]
max_ind = np.argmax(sharpnesses)
slice_to_save = stack_parameters.slice_to_save(max_ind)
# Check the slice corresponds to the index for the first 4 images
assert sharpnesses[slice_to_save] == [496, 569, 454, 333]
# And again for sharpest at the end
sharpnesses = [13, 21, 26, 31, 39, 49, 50, 77, 234, 324, 390, 496, 569]
max_ind = np.argmax(sharpnesses)
slice_to_save = stack_parameters.slice_to_save(max_ind)
# Check the slice corresponds to the index for the final 3 images
assert sharpnesses[slice_to_save] == [390, 496, 569]
def random_capture(set_id: Optional[int] = None):
"""